Beta diversity

From 16S rRNA-gene sequencing of cow SWAB microbiome samples: - 3 timepoints (T0 BEFORE, T0 AFTER AND T8) for SWAB samples and two treatments (oil, treated/untreated)

Between-sample variability from 16S rRna-gene sequencing data.

Clustering

PCA

Clustering by timepoint (PCA):

Clustering by treatment (PCA): after removing samples from timepoint 0 # BECAUSE WE KNOW THAT AT TIMEPOINT 0 WE SHOULD NOT HAVE DIFFERENCES BETWEEN GROUPS

MDS

Clustering by treatment (MDS): NMDS1 vs NMDS2

Clustering by timepoint (MDS):

Clustering by type (MDS): NMDS2 vs NMDS3

Clustering by treatment by timepoint (MDS):

## Warning in metaMDS(matx): stress is (nearly) zero: you may have insufficient
## data

Significance of between-group distances

Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.

Below the ANOVA table from the model:

\[ X = \mu + treatment + timepoint + treatment*type + e \]

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
treatment 1 0.1439951 0.1439951 1.316741 0.0417820 0.111
timepoint 1 0.1309875 0.1309875 1.197795 0.0380077 0.210
residuals 29 3.1713598 0.1093572 NA 0.9202103 NA
total 31 3.4463424 NA NA 1.0000000 NA

going 3D

## Run 0 stress 0.000149963 
## Run 1 stress 9.97299e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001014245  max resid 0.0002806771 
## ... Similar to previous best
## Run 2 stress 9.883956e-05 
## ... New best solution
## ... Procrustes: rmse 4.618237e-05  max resid 0.000195706 
## ... Similar to previous best
## Run 3 stress 9.672124e-05 
## ... New best solution
## ... Procrustes: rmse 4.426533e-05  max resid 0.0001897678 
## ... Similar to previous best
## Run 4 stress 0.00011099 
## ... Procrustes: rmse 3.122843e-05  max resid 8.742987e-05 
## ... Similar to previous best
## Run 5 stress 9.355347e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001013662  max resid 0.0003823866 
## ... Similar to previous best
## Run 6 stress 9.775024e-05 
## ... Procrustes: rmse 8.320419e-05  max resid 0.0002145534 
## ... Similar to previous best
## Run 7 stress 0.0001252052 
## ... Procrustes: rmse 0.0001231785  max resid 0.0004204665 
## ... Similar to previous best
## Run 8 stress 9.677272e-05 
## ... Procrustes: rmse 6.000703e-05  max resid 0.0001955693 
## ... Similar to previous best
## Run 9 stress 9.833002e-05 
## ... Procrustes: rmse 5.248124e-05  max resid 0.0001764376 
## ... Similar to previous best
## Run 10 stress 9.95221e-05 
## ... Procrustes: rmse 0.0001085135  max resid 0.0003993056 
## ... Similar to previous best
## Run 11 stress 9.569179e-05 
## ... Procrustes: rmse 0.000100508  max resid 0.0004735585 
## ... Similar to previous best
## Run 12 stress 9.77646e-05 
## ... Procrustes: rmse 9.442084e-05  max resid 0.0003447424 
## ... Similar to previous best
## Run 13 stress 9.969321e-05 
## ... Procrustes: rmse 0.0001275208  max resid 0.0004873466 
## ... Similar to previous best
## Run 14 stress 8.961434e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001146834  max resid 0.000545623 
## ... Similar to previous best
## Run 15 stress 9.88076e-05 
## ... Procrustes: rmse 0.000164074  max resid 0.0006564917 
## ... Similar to previous best
## Run 16 stress 9.625181e-05 
## ... Procrustes: rmse 0.000159187  max resid 0.0006445011 
## ... Similar to previous best
## Run 17 stress 9.739688e-05 
## ... Procrustes: rmse 0.0001108413  max resid 0.0004631666 
## ... Similar to previous best
## Run 18 stress 9.684643e-05 
## ... Procrustes: rmse 0.0001240389  max resid 0.0003018623 
## ... Similar to previous best
## Run 19 stress 9.712024e-05 
## ... Procrustes: rmse 0.0001625145  max resid 0.0006541186 
## ... Similar to previous best
## Run 20 stress 9.962206e-05 
## ... Procrustes: rmse 0.0001514454  max resid 0.0005570829 
## ... Similar to previous best
## *** Solution reached

timepoint 0 before_oil

timepoint 0 after_oil